Forge Tools bigg_metabolites

bigg_metabolites read

scidex.forge.bigg_metabolites

Query the BiGG Models database (bigg.ucsd.edu) for genome-scale metabolic network metabolites and reactions. BiGG provides 88+ curated organism-specific metabolic reconstructions with 15K+ reactions and 10K+ metabolites, each linked to genes via gene-reaction associations — the foundation of flux balance analysis (FBA) and constraint-based metabolic modeling. query_type='metabolite' (default): search for metabolites by name or BiGG ID; returns formula, charge, compartment distribution, and database cross-refs (KEGG, ChEBI, MetaNetX). query_type='reaction': search for reactions by name or BiGG ID; returns the stoichiometric equation, participating metabolite IDs, associated gene IDs, and organism models. model_id='universal' (default) spans all models; set to a specific BiGG model ID (e.g. 'iJO1366', 'Recon3D') to restrict to one organism. Fills the gap between forge_hmdb_metabolites (chemical properties, no reactions) and forge_rhea_reactions (biochemical ontology, no gene associations). Free public data, no authentication required.

HTTP: POST /api/scidex/forge/bigg_metabolites

Invoke

Calls scidex.tool.invoke on the substrate with this tool name. Edit the JSON below — it must match the input schema. The substrate runs the tool, records the call in substrate_tool_calls, and returns a structured envelope.

Sign in to invoke this tool. Schema and curl snippet are visible to anyone.

Schemas

Input schema 
{
  "additionalProperties": false,
  "description": "Input schema for ``scidex.forge.bigg_metabolites``.",
  "properties": {
    "query": {
      "description": "Search term for the BiGG database. For query_type='metabolite': a metabolite name or BiGG compound ID (e.g. 'atp', 'glucose', 'ATP', 'nadh'). For query_type='reaction': a reaction name or BiGG reaction ID (e.g. 'PFK', 'phosphofructokinase', 'ATPM').",
      "title": "Query",
      "type": "string"
    },
    "query_type": {
      "default": "metabolite",
      "description": "Type of entity to search: 'metabolite' (default) for compounds, or 'reaction' for enzymatic/transport reactions.",
      "title": "Query Type",
      "type": "string"
    },
    "model_id": {
      "default": "universal",
      "description": "BiGG model scope for the search. 'universal' (default) searches the universal set spanning all 88+ curated models. Supply a specific BiGG model ID (e.g. 'iJO1366' for E. coli, 'Recon3D' for human) to restrict results to that organism's reconstruction.",
      "title": "Model Id",
      "type": "string"
    },
    "limit": {
      "default": 20,
      "description": "Maximum number of results to return (1–100). Default 20.",
      "maximum": 100,
      "minimum": 1,
      "title": "Limit",
      "type": "integer"
    }
  },
  "required": [
    "query"
  ],
  "title": "ForgeBiggMetabolitesIn",
  "type": "object"
}
Output schema 
{
  "$defs": {
    "BiggMetabolite": {
      "description": "One BiGG universal metabolite record.",
      "properties": {
        "bigg_id": {
          "description": "BiGG compound identifier (e.g. 'atp', 'nadh', 'glc__D').",
          "title": "Bigg Id",
          "type": "string"
        },
        "name": {
          "description": "Common name of the metabolite.",
          "title": "Name",
          "type": "string"
        },
        "formula": {
          "default": "",
          "description": "Molecular formula (e.g. 'C10H12N5O13P3'). Empty when not in BiGG detail.",
          "title": "Formula",
          "type": "string"
        },
        "charge": {
          "anyOf": [
            {
              "type": "integer"
            },
            {
              "type": "null"
            }
          ],
          "default": null,
          "description": "Formal charge at physiological pH. None when not reported.",
          "title": "Charge"
        },
        "compartments": {
          "description": "Unique compartment BiGG IDs where this metabolite appears across all models (e.g. ['c', 'm', 'e', 'x'] for cytosol, mitochondria, extracellular, peroxisome).",
          "items": {
            "type": "string"
          },
          "title": "Compartments",
          "type": "array"
        },
        "database_links": {
          "additionalProperties": {
            "items": {
              "type": "string"
            },
            "type": "array"
          },
          "description": "Cross-references to external databases. Keys are database names (e.g. 'KEGG Compound', 'ChEBI', 'MetaNetX (MNX) Chemical'); values are lists of accession IDs.",
          "title": "Database Links",
          "type": "object"
        }
      },
      "required": [
        "bigg_id",
        "name"
      ],
      "title": "BiggMetabolite",
      "type": "object"
    },
    "BiggReaction": {
      "description": "One BiGG universal reaction record.",
      "properties": {
        "bigg_id": {
          "description": "BiGG reaction identifier (e.g. 'PFK', 'ATPM', 'EX_glc__D_e').",
          "title": "Bigg Id",
          "type": "string"
        },
        "name": {
          "description": "Common name of the reaction.",
          "title": "Name",
          "type": "string"
        },
        "reaction_string": {
          "default": "",
          "description": "Stoichiometric equation using BiGG metabolite IDs and compartment suffixes (e.g. 'atp_c + f6p_c ↔ adp_c + fdp_c + h_c').",
          "title": "Reaction String",
          "type": "string"
        },
        "metabolites": {
          "description": "BiGG IDs of metabolites participating in this reaction.",
          "items": {
            "type": "string"
          },
          "title": "Metabolites",
          "type": "array"
        },
        "genes": {
          "description": "BiGG gene IDs associated with enzymes catalyzing this reaction.",
          "items": {
            "type": "string"
          },
          "title": "Genes",
          "type": "array"
        },
        "models": {
          "description": "BiGG model IDs (organism reconstructions) that include this reaction.",
          "items": {
            "type": "string"
          },
          "title": "Models",
          "type": "array"
        }
      },
      "required": [
        "bigg_id",
        "name"
      ],
      "title": "BiggReaction",
      "type": "object"
    }
  },
  "description": "Response shape for ``scidex.forge.bigg_metabolites``.",
  "properties": {
    "query": {
      "description": "The search term that was queried.",
      "title": "Query",
      "type": "string"
    },
    "query_type": {
      "description": "Type queried: 'metabolite' or 'reaction'.",
      "title": "Query Type",
      "type": "string"
    },
    "model_id": {
      "description": "BiGG model scope used (e.g. 'universal' or 'iJO1366').",
      "title": "Model Id",
      "type": "string"
    },
    "metabolites": {
      "description": "Matching metabolite records. Populated when query_type='metabolite'. Each record includes formula, charge, compartments, and database cross-refs.",
      "items": {
        "$ref": "#/$defs/BiggMetabolite"
      },
      "title": "Metabolites",
      "type": "array"
    },
    "reactions": {
      "description": "Matching reaction records. Populated when query_type='reaction'. Each record includes the reaction equation, metabolite IDs, genes, and models.",
      "items": {
        "$ref": "#/$defs/BiggReaction"
      },
      "title": "Reactions",
      "type": "array"
    },
    "not_found": {
      "default": false,
      "description": "True when no results were found for the given query.",
      "title": "Not Found",
      "type": "boolean"
    }
  },
  "required": [
    "query",
    "query_type",
    "model_id"
  ],
  "title": "ForgeBiggMetabolitesOut",
  "type": "object"
}

curl snippet

Replace $SCIDEX_JWT with a valid bearer token. Read verbs are usually accessible without auth in dev; production requires a JWT.

curl -sS -X POST '/api/scidex/forge/bigg_metabolites' \
  -H 'authorization: Bearer $SCIDEX_JWT' \
  -H 'content-type: application/json' \
  -d '{
  "query": ""
}'

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